Hacking Next Level Sequencing Machines

We are hacking a HiSeq 2000, Next Level Sequencing Machine. It’s a powerful high-throughput sequencing system that enables large-scale genomics for a broad range of applications. Since more of these machines seem to show up in second hand (there are new machine generations by Illumina) we are trying to reverse engineer them and find new ways to make them work or use them for other purpose.

See thread on Hackteria forum:

And wiki: https://www.hackteria.org/wiki/HiSeq2000_-_Next_Level_Hacking 18



Christopher Burge at Stanford University in California hacked an Illumina sequencer to measure protein–DNA interactions at very high throughput. Nice.

“The GAII is basically a pumping system that pumps things onto the flow cell and then onto a fancy imaging system,”


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Repurposing an Illumina GAIIx sequencer using micro manager.


The GAIIx sequencer is a bit easier to hack in that sense that it uses a 2D camera to acquire images while the HiSeq machines do a TDI (time delay integration) scan with a line CCD. With a special TDI scan software and a PureData sketch we are able to acquire images on the HiSeq, both bright light and fluorescent ( https://www.hackteria.org/wiki/HiSeq2000_-_Next_Level_Hacking#Using_the_HiSeq2000_as_aFluorescent_Scanning_Microscope ). We are now working on integrating the sofware (into micro-manager) to make it easier to use. https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/20

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